In flume experiments, granular avalanches run onto loose substrates develop 3-D architectures that record shear-derived mixing between the flow and the substrate. Spherical silica beads 0.250 mm diameter are run onto stratified substrates of various topographies composed of identical but colored materials. A method of setting and serial sectioning experimental granular deposits is presented. Experiments investigating the interactions between these granular charges and substrates reveal that centimeter-scale vortical reworking features are produced by the highly unsteady flows, with localized erosion depth of the same order as the flow thickness. The structure of the reworking features indicates predominantly bed-normal and streamwise particle motions and is interpreted as most likely to reflect velocity-shear instability growth, similar to Kelvin-Helmholtz instabilities formed in Newtonian fluids. This constitutes the first observation of such features formed within granular fluids by motions within the vertical plane. The scale of the features and degree of mixing generated by them has implications for the reliability of stratigraphic interpretations of geophysical granular flow deposits, such as those formed by debris avalanches and pyroclastic density currents. Sheared “flame structures” commonly observed at the bases of geophysical flow deposits might be explained in some cases by reworking by unsteady currents, or by rapid vertical migration of the active shear zone in long-lived steady currents.